Strong Roots
by NJKaG3
Summary: Naruto on his own trained by Danzo and Hiruzen growing up to challenge his father and his siblings for the title of the strongest future Nau/Ino and different team definited lemons later on this will be a True Godlike Naruto but itll be a bit before he gets there.
1. Chapter 1

**I do not own Naruto in any way or form if I did I'd be on an island with no cell reception instead of on here writing FanFiction.**

**This is one of my first stories and I don't have really any beta readers so I'm just writing my 5 Kage collection of stories and then I'll read all my reviews and rewrite them all one at a time based on that and the repost after I only plan on writing and finishing these 5.**

**This story is going to be different Naruto is not a Jinchuriki of any kind he will be ignored by his parents for his siblings who are Jinchuriki one will be of the Kyuubi and one of the Sanbi and the neglect isn't an intentional thing, Minato and Kushina are still good people. He will go to Danzo for training and eventually branch out through other senseis throughout the story. He will be teamed with Shikamaru and Lee with Gai as his teacher eventually. Naruto/Ino pairing. **

**With all that said please enjoy and write as many reviews as possible for me to improve this as much as I can down the line thank you!**

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**Chapter 1: The Beginning **

"Hi my Name is Naruto Uzumaki-Namikaze I'm the Rokudaime Hokage of Konohagakure no sato a ninja village a village which has just been flattened by a man called Pein well his real Name was Nagato, but he thought he was some sort of badass omnipotent God and changed it to Pein because he thought it was more intimidating, anyway I digress my father and mother perished in the battle as well as 2 of the people that trained me men who I saw as grandfathers and my godfather as well many more died to but Nagato was able to bring most of them back however he ran out of chakra before he could bring everyone back. My Brother Natsu and sister Mito survived though and so did my teammates Shikamaru and Lee and our Jounin-sensei Miato Gai and most of my friends and I got promoted to Hokage so there's that I guess hardly a consolation for all the family I've lost but I'll survive anyway to understand how I got here and how I defeated Pein I have to start with a little background so here we go"

The night of October 10th was cold almost to cold for Konoha standards my Mother Kushina the 2nd Jinchuriki of the Kyuubi and my father the 4th Hokage were both in a specific shelter designed only for my birth that's right today is the day my siblings and I were born. It was a cold and quiet night to much so as I said before but while my mother was pushing us out in a cave hideout somewhere on the outskirts of the village, a masked man claiming to be Madara Uchiha was plotting the village's destruction he planned to release the Kyuubi and Sanbi from their seals the Kyuubi inside my mother who's seal was weakened due to birth and the Sanbi inside my father's old student Rin her seal was always weak as Kiri made it that way to make her a ticking time bomb to destroy the village however he kind and Nobel nature she tried to sacrifice herself by stepping in front of a Jutsu from her teammate Kakashi, that singular action earned the Sanbi's respect he healed her and calmed inside the seal and quit trying to escape allowing her to live and return home.

While Madara is approaching the village my mother finally gives birth to me the last of the three of us and oddly the only blonde. Nastu had crimson red hair and Violet eyes just like mom and Mito did as well I however took after my dad with Blonde hair and blue eyes. Shortly after we came out Madara kidnapped my mother and Rin releasing both bijuu on the village the fight was long and bloody and ultimately my dad tried to use a Jutsu to sacrifice himself and seal the Bijuu into my siblings due to their strong Uzumaki genes they'd handle it much better but Rin knowing she was dying anyway stepped in and took his place the Kyuubi was sealed into Natsu and Sanbi in Mito. My mother survived barely and it took years for her to get back to full strength but Tsunade saved her that night.

The next 4 years were awesome we were all the picture perfect close family going to the park having family game night, getting piggy back rides the usual pillow fights the whole 9 yards but on our birthday that year it all changed you see, being Jinchuriki meant they already even at 4 had chunin level chakra and when they'd get angry would release some of it mixed with Bijuu chakra without realizing it so they had to begin their training. I didn't have a Bijuu in my gut so I didn't need to start yet despite my reserves naturally being almost as high so that's how things continued for 3 years until we all drifted apart sometimes I don't even know if they remember I live with them, now I don't blame them mind you not now not then I never did I could tell they didn't even realize what they were doing but it didn't mean I liked it so I started training myself I'd sneak into my dads study or the old Uzumaki compound considering we lived in the Hokage mansion sometimes I'd even sneak into the Hokage library I learned bits and pieces and grew a lot on my own until one day at 8 years old a man named Danzo found me training and saw my potential so I joined his root organization they created a blood clone of me to stay home while I lived and trained there, if you can call being tortured training.

**First week **during my first week I was put through my first days of emotional conditioning as Danzo called it though mine wasn't as harsh as the others being the Hokage's son it wouldn't be good if I was found emotionless completely aside from that I received kenjutsu and taijutsu training and was taught politics and history.

**Second week **the emotional training continued as well as the other forms from before but I was given a blood transfusion which I didn't know until years later was a combination of Hashirama and Tobirama Senju's DNA they had drawn my blood the first day then proceeded to engineer my Genetic code adding in the Strong water affinity, ability to use mokuton, strong life force and insane chakra control all of this was made much easier being an Uzumaki as my clan was once part of the senju long ago and our close ties allowed my body to accept the changes it took two days of completely draining my blood with a dialysis machine and filling my body with the new blood they made from the cells of the senju along with my own.

**Next two weeks **my affinities were tested I was Found to have Water,Wind,Earth, and Fire affinities a fact which even Danzo almost passed out upon realizing. This began the start of my elemental training where he taught me the **Shadow clone Jutsu **and they split into groups working on soaking,cutting,burning and turning the leaf to dirt while continuing with his past studies.

**Next 10 months **He has mastered the ANBU styles of Kenjutsu and Taijutsu and all 3 levels of nature manipulation he was well versed in history and politics and starting on math and sciences and he had finally graduated from emotional conditioning and learned how to shut them off entirely when on a mission having been sent on about 10 of them and having to kill multiple times he had however developed a heavily sarcastic personality and was overly harsh and ruthless in battle.

**Month 12 **they had me back under the knife again this time he received 2 sharingan eyes the Uchiha massacre had just taken place (yes I realize this is much earlier than cannon but it's an AU for a reason) one of those eyes being from Shusui Uchiha and the other Fugaku who had attained the Mangyeko watching his son Itachi kill his wife just before his own death after they were implanted I was found to have activated EMS and have the ability to turn them on and off an ability that seemed to come from the Namikaze clan being cousins to the Uchiha, before Izuna Uchiha the brother of Madara died he had a fling with a blonde civilian woman in lightning country her son was the founder of the Namikaze clan however no member had ever activated the sharingan but I guess due to how close the DNA was it allowed me to activate EMS. With that a seal was placed over my eyes to make them appear as my original eye color.

**Year 2 **Within the first 6 months I had mastered the Uzumaki styles for Taijutsu and Kenjutsu as well as his father's Taijutsu style and at that point met with Danzo.

Danzo had changed greately perhaps moreso than I did over the last year having someone who actually had emotions around I guess was refreshing for him and slowly he began to open up to me a bit, treating me as close to a grandson as possible for a man like him the other ROOT forces had also began to regain a measure of their emotions as well.

"Naruto you have learned all you can from us it seems we will still call on you for missions from time to time but it would be best if you sought out others to train with and develop even more, I have spoken to Hiruzen and while he was stunned that you had been working with me for so long and had managed to keep your emotions and that I even have become warm to you, he did agree to help as well as Koharu and Homura our old teammates, I encourage you to learn all you can from them from now till the age of 12 when you begin the academy which you will need to attend" stated Danzo in a no nonsense tone while Naruto poured knowing he was already ANBU captain level "Consider this a mission learn all you can from my teammates and then go to the academy keep your full abilities a secret and get close to Sasuke Uchiha he is very much a flight risk, part two is become Hokage after your father he has become far to soft even more so than Hiruzen and I might have learned the value of emotions but I have not forgotten the value of ruthlessness and willingness to annihalte your enemies when need be." Finished Danzo "Hai Danzo-jiji-sama" Naruto said with a smirk.

"Report to the Sarutobi estate tomorrow morning at 6am you will train with my old teammates consistently for the next year and a half after that you will be on your own for the last 6 months before the academy, we will still call on you for missions however" was the last thing Danzo said before sending Naruto on his way.

I trained with Hiruzen and his old teammates for the rest of the year developing his Ninjutsu repertoire and learning sealing he was now 4/10 in the levels of sealing.

**Up until academy **The following years were hard but I picked up where I left off I had thoroughly impressed my 3 new senseis and was still growing half way through my time up until the academy I had learned I had Mokuton by accident during a spar Hiruzen had used a **Shuriken shadow clone Jutsu **to send 300 shuriken at me and I didn't notice until the last minute and I naturally reacted and a wall of wood shot from the ground and saved my life and so I began working on that learning from a man named Tenzo and from clan scrolls Hiruzen had gotten from Tsunade, beyond that I had continued to perfect the styles of each of my sensei and learn even more techniques by the end of the years of training I had mastered my Mokuton and Sealing and all my other techniques and completed countless missions but still nothing higher than B rank as Danzo didn't want to risk the life of the Hokage's son fearing how he'd explain it. Then it came my first day at the academy a school I was way to qualified for but I had a mission one I didn't intend to fail.

**Well there you have it the first person POV will end in next few chapters and go to a normal story style I just want to get through the academy first so by chapter 4 we will be in regular story format.**


	2. Chapter 2

**I do not own Naruto in any way or form if I did I'd be on an island with no cell reception instead of on here writing FanFiction.**

**This is one of my first stories and I don't have really any beta readers so I'm just writing my 5 Kage collection of stories and then I'll read all my reviews and rewrite them all one at a time based on that and the repost after I only plan on writing and finishing these 5.**

**This story is going to be different Naruto is not a Jinchuriki of any kind he will be ignored by his parents for his siblings who are Jinchuriki one will be of the Kyuubi and one of the Sanbi and the neglect isn't an intentional thing, Minato and Kushina are still good people. He will go to Danzo for training and eventually branch out through other senseis throughout the story. He will be teamed with Shikamaru and Lee with Gai as his teacher eventually. Naruto/Ino pairing. **

**With all that said please enjoy and write as many reviews as possible for me to improve this as much as I can down the line thank you!**

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**Chapter 2: Academy days Making friends **

My first day at the academy was a bit anticlimactic after all the hype my parents and all the villagers put into it there was little for me to learn after all my time and training in ROOT and with my other senseis and all my mission experience. However now all was lost as I made my first friends in Rock Lee and Shikamaru Nara as well as Sasuke Uchiha though he was a broody bastard I had a mission and so I made nice.

**Year 1 **they went over the basics history, science, Math, strategy and unlocking chakra as well as chakra control all things I had already done. I made sure to stay in the middle of the pack on purpose but I did show my friends a fraction more of how good I was and helped get them caught up.

**Year 2 **we began to go over the academy 3 basic Jutsu all of which I had mastered long ago and continue to build on what we had the previous year and We also started on Taijutsu while I continued to help my friends.

**Year 3-4 **we continued on improving upon what the academy taught while Naruto and his friends were far past that. Half way through year 3 Lee got diagnosed with a deformity from birth causing his chakra coils to be underdeveloped explaining his issues performing the Jutsus taught at the academy, knowing this Naruto taught him taijutsu and Kenjutsu and sealing telling lee if he could be the best with Shuriken and Kunai as well as Taijutsu and Kenjutsu he could still be a very well rounded shinobi still, prompting him to fan his "flames of youth" as the sensei he found named Maito Gai had told him he began to excel far beyond his years in those fields. My next step was to break Shikamaru of his Laziness and Sasuke of his dark brooding tendencies. The rest of the time continued as normal until the last day at the academy we all passed our exams even Lee who was given special dispensation due to his physical limitation he however proved he could still hang and be a great ninja. Today was the day for team assignments and we will finally jump into our story right as I walked into Iruka-sensei's class that morning at 7am in the middle of a speech.

"Today you become true Genin of Konoha, Heed my words trust and believe in the will of fire listen to your sensei defend your comrades and work hard together and you'll do just fine, with that being said team 1..." Said Iruka as Naruto zoned out.

Speaking of Naruto much had changed and he now sat 5'7 and was 170lbs his hair was similar in length and looks to that of his father who despite it all was still his hero, his face was rounded like that of his mother but much of the baby fat was gone he wore grey ANBU pants with not extra compartments as he used seals to carry ninja tools, he had high black shinobi sandals his forehead protector was worn as a belt as he had seen Lee's sensei Gai wear it and he had taken a liking to he wore a long sleeve fishnet shirt with a short sleeve Black shirt overtop and a necklace with a rope and a Tigers tooth hanging from it over top of this he wore a black leather jacket with orange stripes down both arms and an orange Uzumaki swirl on the back he had two katanas strapped to his back and to complete the outfit he had two black fingerless gloves with metal plates on the back. Underneath it all he had several seals for weapons tattooed on his arms and he had a giant wooden Buddha tattooed on his back and a Large Ape battling a Toad on his right bicep which was a new addition from when Hiruzen had him sign the Monkey contract after graduating.

To Naruto's left was Shikamaru who had also grown and changed he still had the Pineapple style haircut but he was taller standing 5'5 and weighing 160lbs and starting to show some signs of stubble he wore Black Cargo pants with white tape around knees and ankles and short green shinobi sandals, he had a short sleeve fishnet shirt he had his forehead protector tied onto his left shoulder and he had black fingerless gloves like Naruto with plates, overtop of that he had what looked like a Chunin vest but was simply a basic Green ninja vest he had purchased and strapped to his waist was a Kusarigama or chain scythe he would use in conjunction with his shadow attacks and his sealing skills to ensnare enemies and then take them out.

On his right was Lee who was now the tallest at 5'8 he had grown rather muscular weighing in at 190lbs with very little body fat he had emulated his sensei Gai in wearing a green jumpsuit with orange leg warmers and had the extremely bushy eyebrows and bowl cut to match and wore his forehead protector around his waist as well.

(FYI sasukes outfit is the same as Cannon except he added a sword to his back that's it) "Team 7 Sasuke Uchiha , TenTen Higarashi, Kiba Inuzuka ... (_a certain pink haired banshee shrieks In background) _your sensei will be Kakashi Hatake, next Team 8 Hinata Hyūga, Sakura Haruno, Shino Aburame your sensei Kurenai Yuhi, and now Team 9 Natsu Uzumaki-Namikaze , Mito Uzumaki-Namikaze , Neji Hyūga your sensei Kushina Uzumaki" Iruka said and then continued to team 10 but after hearing that Naruto couldn't help but be hurt in all his years in school with his siblings they barely talked and his relationship with his parents was non existent so much so that he wasn't even included on their team and his mother was their sensei and they didn't even think to teach him, oh well he'd show them all what they missed. "Team 10 Ino Yamanka, Choji Akimichi, and Sai Shimura your sensei will be Asuma Sarutobi and finally team 11 Naruto Uzumaki-Namikaze (_at hearing his name his mother and siblings turned around and gasped they had forgotten he even was in their class and he was their own son/brother what kind of people were they)_ Shikamaru Nara, Rock Lee and your sensei will be Maito Gai! Congrats now follow your sensei out to the appropriate training ground and good luck! (Kakashi was on time and all senseis showed up when the teams were announced I figured having his sensei alive to keep him in line would make him more punctual)

**That's that next chapter is their Team test and then first week of Gai's training and some**

**More on how we will whip that Lazy Nara into shape, and also a sprinkling of family drama courtesy of Kushina realizing how much they failed Naruto and Minato coming to the same conclusion. Sorry for the short chapter they'll get longer just needed to get the summarizing and backstory out of the way.**


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